When comparing TotalFinder vs ForkLift 3, the Slant community recommends ForkLift 3 for most people. In the question“What are the best Mac file managers?”ForkLift 3 is ranked 4th while TotalFinder is ranked 5th. The most important reason people chose ForkLift 3 is:

Pro

Easily toggle hidden files

Pro

Built-in application remover

Pro

Rewritten in Swift

Forklift 3 is a significant update from FL2, having been rewritten entirely in Swift.

Cons

Con

Requires special installation procedure in El Capitan and later due to "System Integrity Protection"

"System Integrity Protection" (also know as "Rootless") is a feature introduced in El Capitan that, among other things, inhibits applications to inject code on system apps (TotalFinder injects code into Finder).

For TotalFinder to work properly one must disable SIP temporarly to install. After installation a user can turn SIP back on without issue.